In Sonic Adventure 2, Dr. Eggman broke into Prison Island looking for his grandfather's creation in "Project Shadow", When he finally got to its sleep container, he entered the password (M.A.R.I.A.), and what came out was a hedgehog that the Doctor mistook for his enemy Sonic for a few seconds before Shadow introduced himself. To prove his power, Shadow attacked a G.U.N. robot and destroyed it in a few quick strikes. Shadow then tricked Eggman into giving him the Chaos Emeralds to send Space Colony ARK crashing into Earth. But the ARK was stopped by Super Sonic and... Super Shadow, of all people!

In Shadow the Hedgehog, Eggman created Shadow Androids, which were perfect copies of Shadow with many of his abilities. Eggman attempts to manipulate Shadow in the three-way war among the Black Arms, G.U.N., and Eggman. He even lies to Shadow in several instances, saying he has no past and that he is just another Shadow Android. However, these encounters never turn out the way Eggman expects, as Shadow ends up fighting and defeating him. Recently, Eggman and Shadow have been leaving each other alone, save for a few run-ins and alliances here and there.